Esempio n. 1
0
def main():
    parser = argparse.ArgumentParser('CRAMtools bam-style-index')

    # Logging flags.
    parser.add_argument('-d', '--debug',
        action = 'store_const',
        const = logging.DEBUG,
        dest = 'level',
        help = 'Enable debug logging.',
    )
    parser.set_defaults(level = logging.INFO)

    # Required flags.

    parser.add_argument('-r', '--reference_fasta_path',
                        required = False,
                        help = 'Reference fasta path.',
    )
    parser.add_argument('-b', '--cram_path',
                        required = False,
                        action="append",
                        help = 'Source cram path.',
    )
    parser.add_argument('-u', '--uuid',
                        required = True,
                        help = 'analysis_id string',
    )
    parser.add_argument('--tool_name',
                        required = True,
                        help = 'cramtools'
    )

    args = parser.parse_args()
    tool_name = args.tool_name
    uuid = args.uuid


    logger = pipe_util.setup_logging(tool_name, args, uuid)
    engine = pipe_util.setup_db(uuid)

    hostname = os.uname()[1]
    logger.info('hostname=%s' % hostname)


    if tool_name == 'index':
        cram_path = pipe_util.get_param(args, 'cram_path')
        reference_fasta_path = pipe_util.get_param(args, 'reference_fasta_path')      
        index(uuid, cram_path, reference_fasta_path, engine, logger)
    else:
        sys.exit('No recognized tool was selected')
Esempio n. 2
0
def main():
    parser = argparse.ArgumentParser("picard sortvcf tool")

    # Logging flags.
    parser.add_argument(
        "-d", "--debug", action="store_const", const=logging.DEBUG, dest="level", help="Enable debug logging."
    )
    parser.set_defaults(level=logging.INFO)

    # Tool flags
    parser.add_argument("--case_id", required=True, help="case_id string")
    parser.add_argument("--vcf_path", required=False, action="append")
    parser.add_argument("-out", "--output_vcf", required=False, help="Output VCF name")
    parser.add_argument("--reference_fasta_dict", required=False)
    db = parser.add_argument_group("Database parameters")
    db.add_argument("--host", default="172.17.65.79", help="hostname for db")
    db.add_argument("--database", default="prod_bioinfo", help="name of the database")
    db.add_argument("--postgres_config", default=None, help="postgres config file", required=True)

    # setup required parameters
    args = parser.parse_args()
    case_id = args.case_id

    logger = pipe_util.setup_logging("picard_sortvcf", args, case_id)

    hostname = os.uname()[1]
    logger.info("hostname=%s" % hostname)

    s = open(args.postgres_config, "r").read()
    postgres_config = eval(s)

    DATABASE = {
        "drivername": "postgres",
        "host": args.host,
        "port": "5432",
        "username": postgres_config["username"],
        "password": postgres_config["password"],
        "database": args.database,
    }

    engine = postgres.db_connect(DATABASE)

    vcf_path = pipe_util.get_param(args, "vcf_path")
    reference_fasta_dict = pipe_util.get_param(args, "reference_fasta_dict")
    output_vcf = pipe_util.get_param(args, "output_vcf")
    picard_sortvcf(case_id, vcf_path, output_vcf, reference_fasta_dict, engine, logger)
Esempio n. 3
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def main():
    parser = argparse.ArgumentParser('bamutil docker tool')

    # Logging flags.
    parser.add_argument('-d', '--debug',
        action = 'store_const',
        const = logging.DEBUG,
        dest = 'level',
        help = 'Enable debug logging.',
    )
    parser.set_defaults(level = logging.INFO)
    
    # Required flags.
    parser.add_argument('--tool_name',
                        required = True,
                        help = 'bamutil tool'
    )
    parser.add_argument('--uuid',
                        required = True,
                        help = 'uuid string',
    )
    
    # Tool flags
    parser.add_argument('--bam_path',
                        required = False
    )

    # setup required parameters
    args = parser.parse_args()
    tool_name = args.tool_name
    uuid = args.uuid

    logger = pipe_util.setup_logging(tool_name, args, uuid)
    engine = pipe_util.setup_db(uuid)

    be_lenient = True
    
    if tool_name == 'splitbam':
        bam_path = pipe_util.get_param(args, 'bam_path')
        splitbam(uuid, bam_path, engine, logger)
    else:
        sys.exit('No recognized tool was selected')
        
    return
Esempio n. 4
0
def main():
    parser = argparse.ArgumentParser('GATK MuTect2 Panel Of Normal creation')

    # Logging flags.
    parser.add_argument('-d', '--debug',
        action = 'store_const',
        const = logging.DEBUG,
        dest = 'level',
        help = 'Enable debug logging.',
    )
    parser.set_defaults(level = logging.INFO)

    # Required flags.

    parser.add_argument('-r', '--reference_fasta_path',
                        required = False,
                        help = 'Reference fasta path.',
    )
    parser.add_argument('-rf', '--reference_fasta_fai',
                        required = False,
                        help = 'Reference fasta fai path.',
    )
    parser.add_argument('-snp', '--known_snp_vcf_path',
                        required = False,
                        help='Reference SNP path.',
    )
    parser.add_argument('-cos', '--cosmic_path',
                        required = False,
                        help='Reference COSMIC path.',
    )
    parser.add_argument('-b', '--cram_path',
                        required = False,
                        action="append",
                        help = 'Source cram path.',
    )
    parser.add_argument('-v', '--vcf_path',
                        required = False,
                        action="append",
                        help = 'Individual VCF path',
    )
    parser.add_argument('-j', '--thread_count',
                        required = False,
                        type = is_nat,
                        help = 'Maximum number of threads for execution.',
    )
    parser.add_argument('-bs', '--Parallel_Block_Size',
                        type = is_nat,
                        default = 50000000,
                        required = False,
                        help = 'Parallel Block Size',
    )
    parser.add_argument('-u', '--uuid',
                        required = True,
                        help = 'analysis_id string',
    )
    parser.add_argument('--tool_name',
                        required = True,
                        help = 'gatk tool'
    )

    args = parser.parse_args()
    tool_name = args.tool_name
    uuid = args.uuid
    thread_count = str(args.thread_count)
    Parallel_Block_Size = str(args.Parallel_Block_Size)

    logger = pipe_util.setup_logging('gatk_' + tool_name, args, uuid)
    engine = pipe_util.setup_db(uuid)

    hostname = os.uname()[1]
    logger.info('hostname=%s' % hostname)


    if tool_name == 'mutect2_pon_tool':
        cram_path = pipe_util.get_param(args, 'cram_path')[0]
        known_snp_vcf_path = pipe_util.get_param(args, 'known_snp_vcf_path')
        cosmic_path = pipe_util.get_param(args, 'cosmic_path')
        reference_fasta_path = pipe_util.get_param(args, 'reference_fasta_path')
        thread_count = pipe_util.get_param(args, 'thread_count')
        fai_path = pipe_util.get_param(args, 'reference_fasta_fai')
        blocksize = pipe_util.get_param(args, 'Parallel_Block_Size')
        mutect2_pon_tool.pon(uuid, cram_path, thread_count, reference_fasta_path, cosmic_path, fai_path, blocksize, known_snp_vcf_path, engine, logger)
    elif tool_name == 'CombineVariants':
        vcf_path_list = pipe_util.get_param(args, 'vcf_path')
        reference_fasta_path = pipe_util.get_param(args, 'reference_fasta_path')
        thread_count = pipe_util.get_param(args, 'thread_count')
        CombineVariants.combinevcf(uuid, vcf_path_list, reference_fasta_path, engine, logger)
    else:
        sys.exit('No recognized tool was selected')
Esempio n. 5
0
def main():
    parser = argparse.ArgumentParser('biobambam docker tool')

    # Logging flags.
    parser.add_argument('-d', '--debug',
        action = 'store_const',
        const = logging.DEBUG,
        dest = 'level',
        help = 'Enable debug logging.',
    )
    parser.set_defaults(level = logging.INFO)
    
    # Required flags.
    parser.add_argument('--tool_name',
                        required = True,
                        help = 'biobambam tool'
    )
    parser.add_argument('--uuid',
                        required = True,
                        help = 'uuid string',
    )
    parser.add_argument('--input_state',
                        required = True
    )

    
    # Tool flags
    parser.add_argument('--bam_path',
                        required = False
    )
    parser.add_argument('--reference_fasta_path',
                        required = False
    )

    # setup required parameters
    args = parser.parse_args()
    tool_name = args.tool_name
    uuid = args.uuid
    input_state = args.input_state
    
    logger = pipe_util.setup_logging('biobambam2_' + tool_name, args, uuid)

    sqlite_name =  tool_name + '_' + uuid +'.db'
    engine_path = 'sqlite:///' + sqlite_name
    engine = sqlalchemy.create_engine(engine_path, isolation_level='SERIALIZABLE')

    be_lenient = True
    
    if tool_name == 'bamfixmateinformation':
        bam_path = pipe_util.get_param(args, 'bam_path')
        bamfixmateinformation.bamfixmateinformation(uuid, bam_path, input_state, cpu_count, engine, logger)
    elif tool_name == 'bamindex':
        bam_path = pipe_util.get_param(args, 'bam_path')
        bamindex.bamindex(uuid, bam_path, input_state, engine, logger)
    elif tool_name == 'bammarkduplicates':
        bam_path = pipe_util.get_param(args, 'bam_path')
        bammarkduplicates.bammarkduplicates(uuid, bam_path, input_state, cpu_count, engine, logger)
    elif tool_name == 'bammarkduplicates2':
        bam_path = pipe_util.get_param(args, 'bam_path')
        bammarkduplicates2.bammarkduplicates2(uuid, bam_path, input_state, cpu_count, engine, logger)
    elif tool_name == 'bammdnm':
        bam_path = pipe_util.get_param(args, 'bam_path')
        reference_fasta_path = pipe_util.get_param(args, 'reference_fasta_path')
        bammdnm.bammdnm(uuid, bam_path, reference_fasta_path, input_state, engine, logger)
    elif tool_name == 'bammerge':
        bam_path = pipe_util.get_param(args, 'bam_path')
        bammerge.bammerge(uuid, bam_path, input_state, cpu_count, engine, logger)
    elif tool_name == 'bamsort':
        bam_path = pipe_util.get_param(args, 'bam_path')
        reference_fasta_path = pipe_util.get_param(args, 'reference_fasta_path')
        bamsort.bamsort(uuid, bam_path, reference_fasta_path, input_state, engine, logger)
    elif tool_name == 'bamtofastq':
        bam_path = pipe_util.get_param(args, 'bam_path')
        bamtofastq.bamtofastq(uuid, bam_path, input_state, engine, logger)
    elif tool_name == 'bamvalidate':
        bam_path = pipe_util.get_param(args, 'bam_path')
        bamvalidate.bamvalidate(uuid, bam_path, input_state, cpu_count, engine, logger)
    else:
        sys.exit('No recognized tool was selected')
        
    return